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Series GSE222053 Query DataSets for GSE222053
Status Public on Sep 06, 2023
Title (RNA-seq) Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Understanding mechanisms of epigenetic regulation in embryonic stem cells (ESCs) is of fundamental importance for stem cell and developmental biology. Here we identify Spic, a member of the ETS family of transcription factors, as a specific marker of ground state pluripotency. We show that Spic is rapidly induced in ESCs cultured with GSK3-, MEK-inhibitors and LIF (2iL), and in response to MEK/ERK inhibition. ChIP-seq analysis demonstrated that Spic binds to enhancer elements that are associated with pluripotency genes. Interaction proteomics and genomic profiling confirmed that SPIC interacts with NANOG and stabilizes its binding to chromatin in 2iL-ESCs. Additional gain of function and loss of function experiments revealed that Spic controls genes involved in one carbon (1C) metabolism, Bhmt, Bhmt2, and Dmgdh, and the flux of SAM-to-SAH in 2iL-ESCs. By maintaining low levels of SAM, Spic controls the level of H3K4me3 and H3R17me2 histone methylation in ground state ESCs. Our data highlight the role of uncharacterized axillary transcription factors that link cellular metabolism to epigenetic regulation in ground state pluripotency.
 
Overall design RNA-seq Spic-KO, -OE, and -WT mouse ESCs
Web link https://pubmed.ncbi.nlm.nih.gov/37595034/
 
Contributor(s) Mirzadeh Azad F, Struys E, Wingert V, Hannibal L, Mills K, Jansen J, Longley D, Stunnenberg H, Atlasi Y
Citation(s) 37595034
Submission date Jan 03, 2023
Last update date Dec 08, 2023
Contact name Yaser Atlasi
E-mail(s) y.atlasi@qub.ac.uk
Organization name Queen's University Belfast
Department patrick G Johnston Centre for Cancer research
Street address Lisburn Road
City Belfast
ZIP/Postal code BT9 7AE
Country United Kingdom
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (10)
GSM6912760 RNA-seq-21-spic_OE_2iD1_cl5
GSM6912761 RNA-seq-22-spic_OE_2iD1_cl6
GSM6912762 RNA-seq-23-E14_2iD1_Rep1
This SubSeries is part of SuperSeries:
GSE222058 Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency
Relations
BioProject PRJNA917519

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE222053_RAW.tar 1.0 Gb (http)(custom) TAR (of BEDGRAPH, BW)
GSE222053_Spic_RNA_2iLd20_analysis.xlsx 4.7 Mb (ftp)(http) XLSX
GSE222053_processed_file_RNA-seq.xlsx 2.6 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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